gene set (enrichment) analysis
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Bogdan ▴ 620
@bogdan-2367
Last seen 5 days ago
Palo Alto, CA, USA

Dear all,

 

please could you advise about the best BioC/R package to use for gene set enrichment analysis ;)

on a side note, may I ask the same question about the easiest package to use for survival analysis :)

many thanks,

-- bogdan

 

 

gsea gsa • 1.0k views
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have you tried the gsea package from the broad institute?

or the gage package 

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b.nota ▴ 340
@bnota-7379
Last seen 10 months ago
Netherlands

I recommend the GOseq package for GO enrichment analysis, it's quite easy in use if you read the manual first. You only need a list of your significant genes and a list of all your assayed genes.

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Bogdan ▴ 620
@bogdan-2367
Last seen 5 days ago
Palo Alto, CA, USA

thank you !

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Axel Klenk ▴ 980
@axel-klenk-3224
Last seen 14 hours ago
Switzerland

Dear Bogdan,

I'm a bit late for your question but I think the limma package must be mentioned: see the help pages for camera, roast and romer. These are gene set tests, not enrichment tests, i.e., no DEG list required.

Cheers,

 - axel

 

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thanks Axel !

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